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README.md

Making a glass brain

NeuroSnippets made-with-bash

This bash script generates a glass brain from diffusion MRI data as described in this post.

To run it, you need the following tools:

  • git-annex (7.20190819);
  • datalad (0.11.8);
  • MRtrix3 (3.0-RC3);
  • FSL (6.0);
  • TractSeg (2.2).

The script was tested on Ubuntu 18.04.

Some things to keep in mind:

  • the script foreach provided in MRtrix3 has been renamed to for_each in more recent versions to avoid conflicts with zsh in macOS - if you are using the most up-to-date version, please update the script accordingly;
  • the script dwipreproc used to run eddy in MRtrix3 has been renamed to dwifslpreproc in more recent versions - if you are using the most up-to-date version, please update the script accordingly;
  • a counter-intuitive fun fact: to align the tractography in subject space with the template, the script uses the inverse warp (from template to subject).